SMTL ID : 2vjy.1 (1 other biounit)

Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Chain B: P.26, G.27, E.51, T.73, V.76, H.115 Ligands: MG.2, ALK.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.415, A:L.449, A:Y.474, A:I.476, A:E.477 Hydrogen bonds: A:T.390, A:G.413, A:I.415, A:G.443, A:G.445, A:S.446, A:N.471, A:T.475, A:T.475, A:I.476 Water bridges: A:T.390, A:S.391, A:D.444, A:S.446, A:S.446 TPP.6: 23 residues within 4Å: Chain A: P.26, G.27, E.51, V.76, H.115 Chain B: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Ligands: MG.7, ALK.8 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.415, B:I.415, B:L.449, B:Y.474, B:Y.474, B:I.476, B:E.477, A:V.76 Hydrogen bonds: B:T.390, B:T.390, B:G.413, B:I.415, B:G.443, B:G.445, B:S.446, B:N.471, B:G.473, B:T.475, B:I.476 Water bridges: B:T.390, B:S.391, B:D.444, B:S.446, B:S.446

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.444, N.471, G.473, T.475 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.10 MG.7: 4 residues within 4Å: Chain B: D.444, N.471, G.473 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.24

4 x ALK: methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid(Non-covalent)(Covalent)

ALK.3: 9 residues within 4Å: Chain A: F.292, T.388, E.477, I.480 Chain B: G.27, D.28, H.114, H.115 Ligands: TPP.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.28 Water bridges: B:F.29, B:F.29 Hydrophobic interactions: A:T.388 ALK.4: 7 residues within 4Å: Chain A: H.92, C.221, H.225, G.286, A.287, H.310, S.311 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.225, A:H.310, A:S.311, A:S.311 Water bridges: A:D.312, A:Y.313 ALK.8: 9 residues within 4Å: Chain A: G.27, D.28, H.114, H.115 Chain B: F.292, T.388, E.477, I.480 Ligands: TPP.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.28, A:D.28, A:H.115 Water bridges: A:F.29, A:F.29 Hydrophobic interactions: B:T.388 ALK.9: 7 residues within 4Å: Chain B: H.92, C.221, H.225, G.286, A.287, H.310, S.311 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.225, B:H.310, B:S.311 Water bridges: B:D.312

2 x ALU: METHYL HYDROGEN (S)-ACETYLPHOSPHONATE

ALU.5: 6 residues within 4Å: Chain A: Q.16, V.17, E.18, K.65, Y.157, L.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.18 Water bridges: A:M.67 ALU.10: 5 residues within 4Å: Chain B: V.17, E.18, K.65, G.66, Y.157 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.157 Hydrogen bonds: B:K.65 Water bridges: B:M.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kutter, S. et al., Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation. J.Biol.Chem. (2009)

Release Date

2009-01-27

Peptides

PYRUVATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE DECARBOXYLASE

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